Showing : comBat • reset
1
vote
2
replies
323
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
4 months ago takemoto • 0
0
votes
1
reply
201
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 5 months ago by 46k • written 5 months ago by • 0
1
vote
4
replies
1.8k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
12 months ago NewBioInfo ▴ 10
4
votes
4
replies
520
views
Combat and dds Object
DESeq2 combat
updated 14 months ago by 3.6k • written 14 months ago by ▴ 20
0
votes
0
replies
297
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
18 months ago joannew • 0
1
vote
3
replies
554
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 19 months ago by 3.6k • written 19 months ago by • 0
1
vote
8
replies
714
views
Error in running Combat function
sva ComBat
updated 20 months ago by 3.6k • written 21 months ago by ▴ 10
0
votes
5
replies
475
views
Variable of interest in combat correction
sva combat
updated 23 months ago by 61k • written 23 months ago by ▴ 10
0
votes
3
replies
447
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 2.0 years ago by 3.6k • written 2.0 years ago by • 0
7
votes
6
replies
617
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 2.4 years ago by ▴ 840 • written 2.4 years ago by ▴ 10
1
vote
2
replies
422
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 2.7 years ago by 46k • written 2.7 years ago by • 0
0
votes
0
replies
977
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
2.8 years ago anne.bozack • 0
0
votes
1
reply
431
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 2.8 years ago by 3.6k • written 2.8 years ago by • 0
0
votes
1
reply
428
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 2.8 years ago by ▴ 840 • written 2.8 years ago by ▴ 10
0
votes
3
replies
501
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 2.9 years ago by 25k • written 2.9 years ago by • 0
8
votes
18
replies
7.6k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 19 months ago by • 0 • written 3.0 years ago by ▴ 10
2
votes
2
replies
673
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 3.0 years ago by 38k • written 3.0 years ago by ▴ 10
2
votes
3
replies
526
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 3.1 years ago by ★ 1.1k • written 3.1 years ago by ▴ 50
0
votes
2
replies
504
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 3.1 years ago by 38k • written 3.1 years ago by • 0
0
votes
0
replies
392
views
The correct specification of the model matrix to ComBat
ComBat sva
3.1 years ago Sam ▴ 10
0
votes
6
replies
1.1k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 3.1 years ago by ▴ 260 • written 3.2 years ago by ▴ 640
7
votes
4
replies
2.6k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 3.2 years ago by 46k • written 3.2 years ago by ▴ 640
4
votes
16
replies
1.6k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 3.3 years ago by 38k • written 3.3 years ago by ▴ 10
3
votes
12
replies
1.7k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 3.4 years ago by 61k • written 3.4 years ago by ▴ 10
0
votes
0
replies
465
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 4.0 years ago by 46k • written 4.0 years ago by • 0
0
votes
2
replies
852
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 4.1 years ago by 38k • written 4.1 years ago by • 0
0
votes
0
replies
516
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
4.1 years ago jmsendoya • 0
0
votes
1
reply
1.1k
views
A problem in using Combat
sva combat
updated 4.3 years ago by ▴ 840 • written 4.3 years ago by • 0
1
vote
1
reply
1.7k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 4.7 years ago by 46k • written 7.6 years ago by ▴ 130
1
vote
9
replies
1.5k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
4.7 years ago jaro.slamecka ▴ 130
0
votes
8
replies
1.5k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 4.8 years ago by • 0 • written 7.2 years ago by • 0
0
votes
0
replies
644
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
5.0 years ago Eddie Imada • 0
0
votes
1
reply
676
views
Combat prior plots good enough?
combat combat sva
5.0 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
1.6k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 5.0 years ago by ▴ 840 • written 5.0 years ago by • 0
2
votes
5
replies
3.8k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 5.0 years ago by ★ 27k • written 5.0 years ago by ▴ 20
1
vote
1
reply
1.4k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 5.2 years ago by 61k • written 5.2 years ago by ▴ 10
0
votes
0
replies
994
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
5.2 years ago DataFanatic ▴ 10
0
votes
4
replies
1.6k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 5.3 years ago by 38k • written 5.3 years ago by • 0
0
votes
0
replies
891
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
5.4 years ago svlachavas ▴ 800
1
vote
1
reply
673
views
How to interpret the SVA results
SVA combat RNA-seq
updated 5.5 years ago by 61k • written 5.5 years ago by • 0
10
votes
4
replies
2.0k
views
Adjust for multiple batches using combat
combat sva limma
updated 5.6 years ago by ★ 27k • written 5.6 years ago by • 0
3
votes
4
replies
2.0k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 5.6 years ago by 38k • written 5.6 years ago by ▴ 10
0
votes
0
replies
750
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
5.6 years ago Ryan C. Thompson 7.8k
0
votes
6
replies
1.1k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
6.0 years ago User34591 • 0
5
votes
2
replies
6.2k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 6.0 years ago by ▴ 70 • written 6.0 years ago by ▴ 30
5
votes
3
replies
2.9k
views
about SVA: matrix of corrected expression values
SVA COMBAT
6.0 years ago Bogdan ▴ 640
3
votes
8
replies
1.5k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 6.1 years ago by ▴ 30 • written 6.1 years ago by • 0
13
votes
2
replies
2.4k
views
voom with combat
limma voom combat batch effect
updated 6.2 years ago by 46k • written 6.2 years ago by ▴ 10
0
votes
1
reply
768
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 6.2 years ago by ▴ 400 • written 6.2 years ago by ▴ 800
48
votes
20
replies
33k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 6.3 years ago by • 0 • written 6.8 years ago by ▴ 100
50 results • Page 1 of 1
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Answer: Caching bam index files using BiocFileCache by shepherl 3.3k
It is now possible to override the unique identifier addition. Unique identifiers are still the default. See https://github.com/Bioconduc…
Comment: Help with differential gene expression using Agilent Microarray data (from GEO d by James W. MacDonald 61k
You can also use `GEOquery` to get the raw data if available. Unfortunately, what the submitter uploaded as 'raw' data in this instance is …
Comment: Help with differential gene expression using Agilent Microarray data (from GEO d by r02eb20 • 0
Thank you so much! Also, I didn't realise it was easier to use GEOquery rather than actually reading the data file in - I will definitely…
Answer: Help with differential gene expression using Agilent Microarray data (from GEO d by James W. MacDonald 61k
I would use `GEOquery` to get the data. ``` > dat <- getGEO("GSE104438")[[1]] ## now you have to get rid of some extra cruft > na…
Answer: Correcting for all the comparisons that have been made in analysis by James W. MacDonald 61k
You have already noted that `DESeq2` automatically adjusts for the multiplicity within each comparison. So I presume you are not asking how…
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Answer: Correcting for all the comparisons that have been made in analysis
A: How do I get groseq signal for each gene from groSeq in groHMM
A: How do I get groseq signal for each gene from groSeq in groHMM
How do I get groseq signal for each gene from groSeq in groHMM
How do I get groseq signal for each gene from groSeq in groHMM
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